Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.

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State: Public
Version: Final published version
License: CC BY-NC-ND 4.0
Serval ID
serval:BIB_ACC82F5026CE
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.
Journal
HGG advances
Author(s)
Lepamets M., Auwerx C., Nõukas M., Claringbould A., Porcu E., Kals M., Jürgenson T., Morris A.P., Võsa U., Bochud M., Stringhini S., Wijmenga C., Franke L., Peterson H., Vilo J., Lepik K., Mägi R., Kutalik Z.
Working group(s)
Estonian Biobank Research Team
ISSN
2666-2477 (Electronic)
ISSN-L
2666-2477
Publication state
Published
Issued date
13/10/2022
Peer-reviewed
Oui
Volume
3
Number
4
Pages
100133
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
Copy-number variations (CNV) are believed to play an important role in a wide range of complex traits, but discovering such associations remains challenging. While whole-genome sequencing (WGS) is the gold-standard approach for CNV detection, there are several orders of magnitude more samples with available genotyping microarray data. Such array data can be exploited for CNV detection using dedicated software (e.g., PennCNV); however, these calls suffer from elevated false-positive and -negative rates. In this study, we developed a CNV quality score that weights PennCNV calls (pCNVs) based on their likelihood of being true positive. First, we established a measure of pCNV reliability by leveraging evidence from multiple omics data (WGS, transcriptomics, and methylomics) obtained from the same samples. Next, we built a predictor of omics-confirmed pCNVs, termed omics-informed quality score (OQS), using only PennCNV software output parameters. Promisingly, OQS assigned to pCNVs detected in close family members was up to 35% higher than the OQS of pCNVs not carried by other relatives (p < 3.0 × 10 <sup>-90</sup> ), outperforming other scores. Finally, in an association study of four anthropometric traits in 89,516 Estonian Biobank samples, the use of OQS led to a relative increase in the trait variance explained by CNVs of up to 56% compared with published quality filtering methods or scores. Overall, we put forward a flexible framework to improve any CNV detection method leveraging multi-omics evidence, applied it to improve PennCNV calls, and demonstrated its utility by improving the statistical power for downstream association analyses.
Keywords
PennCNV, anthropometric traits, copy-number variation, gene expression, methylation, multi-omics, structural variation, whole genome sequencing
Pubmed
Open Access
Yes
Create date
05/09/2022 8:17
Last modification date
17/09/2022 5:34
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